The circadian clock is a biological system providing an internal self-sustained temporal framework and adaptation mechanisms to the daily environmental rhythm. One of its behavioral implication in humans is the sleep-wake cycle. The core mammalian circadian clock is a system composed of interacting regulatory feedback loops present in many tissues throughout the body. The core set of circadian clock genes codes for proteins feeding back to regulate not only their own expression, but also that of clock output genes and regulatory pathways. Still, however, our understanding of processes regulated in a circadian fashion and the linkage between the molecular system and behavioral or physiological outputs is poor. Our work aims at identification of clock-controlled genes (CCGs) and their regulatory motifs. We analyzed several microarray measurements of genes with a daily oscillating expression and extracted 2065 of them together with their peak expression phases and oscillation amplitudes. For an in-depth analysis we selected a subset of 167 genes reported by multiple microarray experiments. Gene promoters were scanned in the search for known regulatory motifs of clock genes (E-Box, RRE, D-Box, CRE) as well as other over-represented regulatory motifs. We found an over-representation of the E-boxes and D-boxes in the selected subset of 167 CCGs. This over-representation is smaller when the list of 2065 genes is analyzed. The search for other regulatory motifs contained in the TRANSFAC database revealed a strong over-representation of some of them such as Spl, AP-2, STAT1, HIF-1 and E2F. The signals found in the promoter sequences indicate possible regulatory mechanisms important for the coordination of circadian rhythms.